RStudio is an Integrated Development Environment (IDE) for the R language. By containerizing RStudio, a scientist can leverage the reproducibility and portability of the Singularity platform, allowing them to build data visualizations and analysis tools and ensure that they behave exactly the same in a new environment.
The Singularity definition (def) file is:
Bootstrap: library
From: debian:9
%environment
LC_ALL="C"
export LC_ALL
%post
apt-get update
apt-get -y install systemd systemd-sysv gdebi-core procps libssl1.1 ed wget curl libqt5webkit5 libqt5core5a
apt-get -y install r-base r-base-dev
curl https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb > /rstudio-1.1.456-amd64.deb
apt-get -y install /rstudio-1.1.456-amd64.deb
wget -O /rstudio-server-stretch-1.1.456-amd64.deb \
https://download2.rstudio.org/rstudio-server-stretch-1.1.456-amd64.deb
gdebi -n /rstudio-server-stretch-1.1.456-amd64.deb
# Setup the "general" CRAN repo
echo 'local({
r <- getOption("repos")
r["CRAN"] = "https://cran.us.r-project.org"
options(repos = r)
})' >> /etc/R/Rprofile.site
# We are setting up a normal user for access
# Login: rstudio Password: rstudio
useradd -c "RStudio Account" -u 500 -d /home/rstudio -s /bin/bash rstudio
echo "rstudio:rstudio" | /usr/sbin/chpasswd
# Move systemd service file into place
cp /usr/lib/rstudio-server/extras/systemd/rstudio-server.service /lib/systemd/system/
systemctl enable rstudio-server
# Remove unneeded source packages
rm -f /rstudio-1.1.456-amd64.deb
rm -f /rstudio-server-stretch-1.1.456-amd64.deb
%runscript
/usr/bin/rstudio "$@"
%startscript
/usr/lib/rstudio-server/bin/rserverThe definiton file affords some flexibility, allowing you to run RStudio several different ways:
This will start up rstudio-server, on default port of 8787
$ singularity instance start rstudio.sif rsThis will run rstudio IDE
$ singularity run rstudio.sifAny program in the container, but specifically for running R directly.
$ singularity exec rstudio.sif R -f myfile.rTo build the image run:
$ sudo singularity build rstudio.sif rstudio.defWhen you use run for the IDE, you may need to execute it like:
$ SINGULARITYENV_DISPLAY=${DISPLAY} \
singularity run rstudio.sifThis is needed only if the DISPLAY environment variable does not automatically propagate from your host environment to the container.
For a modification of rstudio-server, you can create a rstudio.conf file, and bind mount it into the container. For example to run on port 9999:
$ echo "www-port=9999" > rserver.conf
$ singularity instance start \
-B rserver.conf:/etc/rstudio/rserver.conf \
rstudio.sif rsYou will then access your rstudio-server instance at: https://localhost:9999
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